Ecological transformation is an inevitable trend for the development of land consolidation (LC) worldwide, and the research on carbon effect of LC is an important theoretical basis for promoting the construction of Eco-LC. However, there is currently a lack of analysis of the carbon effect based on the whole process of LC, ignoring the stage elements and temporal factors. This study applied Life Cycle Assessment (LCA) method to construct a research framework and accounting system for carbon footprint assessment of LC, and explored the carbon effect in a typical land consolidation project area (LCPA) of China. Results showed that: (a) The carbon effect of the project area was characterized as carbon emission during the whole life cycle of LC. Carbon footprint before and after LC was 3.251 tCE·ha−1·a−1 and 2.401 tCE·ha−1·a−1 respectively. The carbon storage reduced and the carbon footprint is declined by 0.850 tCE·ha−1·a−1. (b) Carbon effect varied among different stages of LC. The Benefit Period (BP) was the only stage that was manifested as carbon absorption (−14.65%), while all the other stages were manifested as carbon emission. Among them, as to the carbon emission, the Construction Period (CP) played a decisive role with the most proportion (102.74%), followed by DP and RP, and the carbon effect of PP was negligible. (c) The dominant factors of carbon effect at different stages were also different. During CP, cement contributed the most to the carbon emission in this case. During RP, carbon sequestration effect of cropland proved to be the most significant. During RP, the carbon sequestration effect of cultivated land and the carbon emission effect of unused land were the most prominent. During BP, the carbon sequestration capacity of farmland ecosystems proved to be greater than the carbon emissions from agricultural activities. This study contributes to providing certain theoretical guidance and method reference for the realization of Low-Carbon LC project planning, with this comprehensive and reliable method.